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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ), 'gf_id' => 'HOM05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001174' ), 'data_identifier' => 'HOM05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13500' => 'bna', 'A02p32350' => 'bna', 'A06p44100' => 'bna', 'A10p18540' => 'bna', 'Aa31LG1G13270' => 'aar', 'Aa31LG2G2880' => 'aar', 'Aa31LG2G8100' => 'aar', 'Aa31LG9G11790' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.679' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.680' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1609' => 'aag', 'Actinidia12241' => 'ach', 'Actinidia13745' => 'ach', 'Actinidia16540' => 'ach', 'Actinidia17192' => 'ach', 'Actinidia20104' => 'ach', 'Actinidia30852' => 'ach', 'Ah.01g004360' => 'amhyb', 'Ah.02g118110' => 'amhyb', 'Ah.02g118200' => 'amhyb', 'AL1G47810' => 'aly', 'AL2G23810' => 'aly', 'AL3G44380' => 'aly', 'AL5G10920' => 'aly', 'AL6G33260' => 'aly', 'Aqoxy2G00515' => 'aox', 'Aqoxy2G00632' => 'aox', 'Aqoxy2G04064' => 'aox', 'Aqoxy385s002' => 'aox', 'Aqoxy3G00778' => 'aox', 'Aqoxy3G03998' => 'aox', 'Aqoxy6G00024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0IX9E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LCL4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7R2T36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D3EZ0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DXS2NJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4SVGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JPX7RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LCQF6T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM7VB5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TL38SF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TP2IXW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSBJ8P' => 'arhy', 'AT1G33420' => 'ath', 'AT1G66170' => 'ath', 'AT2G01810' => 'ath', 'AT2G07714' => 'ath', 'AT5G22260' => 'ath', 'ATMG00550' => 'ath', 'ATR0021G014' => 'atr', 'ATR0021G020' => 'atr', 'ATR0021G049' => 'atr', 'ATR0598G035' => 'atr', 'ATR0598G213' => 'atr', 'ATR0804G001' => 'atr', 'ATR0804G002' => 'atr', 'ATR0804G016' => 'atr', 'ATR0804G051' => 'atr', 'ATR0804G065' => 'atr', 'ATR0804G068' => 'atr', 'ATR0804G085' => 'atr', 'ATR0804G091' => 'atr', 'ATR1089G105' => 'atr', 'Atru.chr1.2010' => 'acertr', 'Atru.chr11.817' => 'acertr', 'Atru.chr11.992' => 'acertr', 'Atru.chr3.1455' => 'acertr', 'AUR62000584' => 'cqu', 'AUR62000609' => 'cqu', 'AUR62006941' => 'cqu', 'AUR62006960' => 'cqu', 'AUR62037364' => 'cqu', 'AUR62042690' => 'cqu', 'BcaB03g13700' => 'bca', 'BcaB05g24156' => 'bca', 'BcaB07g30373' => 'bca', 'BcaB08g36444' => 'bca', 'BcaC03g14733' => 'bca', 'BcaC03g17075' => 'bca', 'BcaC04g19562' => 'bca', 'BcaC06g31277' => 'bca', 'BcaC06g34117' => 'bca', 'BolC2t08313H' => 'bol', 'BolC2t11072H' => 'bol', 'BolC2t11073H' => 'bol', 'BolC7t43779H' => 'bol', 'BolC9t58308H' => 'bol', 'BraA02t06408Z' => 'bra', 'BraA02t08252Z' => 'bra', 'BraA06t27284Z' => 'bra', 'BraA10t43934Z' => 'bra', 'C02p21800' => 'bna', 'C02p49930' => 'bna', 'C02p49940' => 'bna', 'C07p32520' => 'bna', 'C09p54390' => 'bna', 'CAN.G222.78' => 'can', 'CAN.G407.108' => 'can', 'CAN.G458.17' => 'can', 'CAN.G7.10' => 'can', 'CANSAT54G1561' => 'cansat', 'CANSAT78G1402' => 'cansat', 'CANSAT78G2060' => 'cansat', 'CARHR032870' => 'chi', 'CARHR144360' => 'chi', 'CARHR191300' => 'chi', 'CARHR282920' => 'chi', 'CARHR287150' => 'chi', 'CARHR292300' => 'chi', 'Carub.0001s3162' => 'cru', 'Carub.0002s1216' => 'cru', 'Carub.0005s0077' => 'cru', 'Carub.0006s2000' => 'cru', 'Ca_00234_v3' => 'car', 'Ca_04796_v3' => 'car', 'Ca_05841_v3' => 'car', 'Ca_09902_v3' => 'car', 'Ca_25248_v3' => 'car', 'CBR_g139' => 'cbr', 'CBR_g48708' => 'cbr', 'Cc00_g27260' => 'ccan', 'Cc07_g13160' => 'ccan', 'Cc11_g05640' => 'ccan', 'Cc11_g06440' => 'ccan', 'CDE05G0825' => 'cde', 'CDE05G0880' => 'cde', 'CDE05G2044' => 'cde', 'CDE05G2153' => 'cde', 'CDE05G2775' => 'cde', 'CDE05G2984' => 'cde', 'CDE05G3524' => 'cde', 'Cfa007781' => 'cfa', 'Cfa010455' => 'cfa', 'Cfa020921' => 'cfa', 'Cfa021493' => 'cfa', 'Cfa022224' => 'cfa', 'Cfa026492' => 'cfa', 'Ciclev10007029m.g' => 'ccl', 'Ciclev10017749m.g' => 'ccl', 'Ciclev10017892m.g' => 'ccl', 'Ciclev10025026m.g' => 'ccl', 'CiPaw.03G074800' => 'cil', 'CiPaw.04G008200' => 'cil', 'CiPaw.06G058200' => 'cil', 'CiPaw.16G119600' => 'cil', 'ClCG00G004060' => 'cla', 'ClCG04G002710' => 'cla', 'ClCG10G001160' => 'cla', 'ClCG11G001060' => 'cla', 'ClCG11G001090' => 'cla', 'COL.COLO4_09221' => 'col', 'COL.COLO4_34460' => 'col', 'COL.COLO4_35284' => 'col', 'COL.COLO4_35484' => 'col', 'Cpa.g.sc138.43' => 'cpa', 'Cpa.g.sc165.19' => 'cpa', 'Cpa.g.sc165.20' => 'cpa', 'Cpa.g.sc2.119' => 'cpa', 'Cpa.g.sc2.163' => 'cpa', 'Cpa.g.sc249.16' => 'cpa', 'Cpa.g.sc87.13' => 'cpa', 'Cpa.g.sc87.35' => 'cpa', 'Cpa.g.sc87.36' => 'cpa', 'Cpa.g.sc87.7' => 'cpa', 'Cpa.g.sc87.9' => 'cpa', 'Cre03.g148250' => 'cre', 'CsaV3_3G001180' => 'csa', 'CsaV3_4G029980' => 'csa', 'CsaV3_5G013130' => 'csa', 'CSS0035790' => 'camsi', 'CSS0039299' => 'camsi', 'CSS0048326' => 'camsi', 'CSS0050231' => 'camsi', 'DCAR_013187' => 'dca', 'DCAR_013188' => 'dca', 'DCAR_014154' => 'dca', 'DCAR_014155' => 'dca', 'DCAR_014156' => 'dca', 'DCAR_026824' => 'dca', 'DCAR_030292' => 'dca', 'Dinv05358' => 'din', 'Dinv09545' => 'din', 'Dinv20497' => 'din', 'Dinv20545' => 'din', 'Dinv22066' => 'din', 'Dinv26829' => 'din', 'Dinv28177' => 'din', 'Duzib093G1066' => 'dzi', 'Duzib147G0032' => 'dzi', 'Duzib177G1126' => 'dzi', 'Duzib205G0700' => 'dzi', 'ECA233G1027' => 'eca', 'ECA233G4976' => 'eca', 'ECA233G6154' => 'eca', 'ECA234G1941' => 'eca', 'ECA240G2300' => 'eca', 'EL10Ac4g09712' => 'bvu', 'EL10Ac4g09733' => 'bvu', 'EL10Ac9g20685' => 'bvu', 'Eucgr.B02649' => 'egr', 'Eucgr.F04095' => 'egr', 'Eucgr.G02081' => 'egr', 'Eucgr.I00019' => 'egr', 'Eucgr.J01622' => 'egr', 'Eucgr.J01636' => 'egr', 'FAN02G3809' => 'fan', 'FAN05G0569' => 'fan', 'FAN07G2037' => 'fan', 'FAN08G3192' => 'fan', 'FAN12G4062' => 'fan', 'FAN14G1145' => 'fan', 'FAN14G3328' => 'fan', 'FAN17G2170' => 'fan', 'FAN19G1419' => 'fan', 'FAN19G2209' => 'fan', 'FAN19G2507' => 'fan', 'FAN20G0517' => 'fan', 'FAN20G0723' => 'fan', 'FAN20G1181' => 'fan', 'FAN20G2593' => 'fan', 'FAN22G1627' => 'fan', 'FAN23G0797' => 'fan', 'FAN23G2924' => 'fan', 'FAN24G1382' => 'fan', 'FAN26G0168' => 'fan', 'FAN26G1916' => 'fan', 'FAN28G1611' => 'fan', 'FAN28G1665' => 'fan', 'FvH4_1g25980' => 'fve', 'FvH4_1g29990' => 'fve', 'FvH4_2g00220' => 'fve', 'FvH4_4g29671' => 'fve', 'FvH4_4g35820' => 'fve', 'FvH4_6g02390' => 'fve', 'Glyma.01G047400' => 'gma', 'Glyma.02G107600' => 'gma', 'Glyma.02G243200' => 'gma', 'Glyma.09G233500' => 'gma', 'Glyma.10G176200' => 'gma', 'Glyma.12G003300' => 'gma', 'Glyma.14G212300' => 'gma', 'Glyma.20G214100' => 'gma', 'Gohir.A02G108901' => 'ghi', 'Gohir.A08G231000' => 'ghi', 'Gohir.A10G158722' => 'ghi', 'Gohir.A12G228200' => 'ghi', 'Gohir.D03G062000' => 'ghi', 'Gohir.D08G251400' => 'ghi', 'Gohir.D10G109800' => 'ghi', 'Gohir.D12G230700' => 'ghi', 'Gorai.004G268100' => 'gra', 'Gorai.008G246900' => 'gra', 'Gorai.011G120900' => 'gra', 'Gorai.013G106900' => 'gra', 'GSVIVG01000247001' => 'vvi', 'GSVIVG01011588001' => 'vvi', 'GSVIVG01030666001' => 'vvi', 'GSVIVG01037120001' => 'vvi', 'HanXRQChr03g0091961' => 'han', 'HanXRQChr08g0224311' => 'han', 'HanXRQChr08g0224541' => 'han', 'HanXRQChr13g0422081' => 'han', 'HanXRQChr15g0483001' => 'han', 'Haze_03409' => 'cav', 'Haze_10803' => 'cav', 'Haze_14016' => 'cav', 'Haze_14291' => 'cav', 'Haze_19356' => 'cav', 'Hma1.2p1_0049F.1_g028520' => 'hma', 'Hma1.2p1_0066F.1_g035730' => 'hma', 'Hma1.2p1_0895F.1_g233720' => 'hma', 'Hma1.2p1_1223F.1_g268420' => 'hma', 'Hma1.2p1_1450F.1_g284190' => 'hma', 'Hma1.2p1_1525F.1_g288890' => 'hma', 'Hma1.2p1_2053F.1_g312730' => 'hma', 'HPP92_001195' => 'vpl', 'HPP92_002292' => 'vpl', 'HPP92_009316' => 'vpl', 'HPP92_009317' => 'vpl', 'Hund21763' => 'sun', 'Lalb_Chr02g0149781' => 'lal', 'Lalb_Chr02g0149791' => 'lal', 'Lalb_Chr02g0149801' => 'lal', 'Lalb_Chr06g0168761' => 'lal', 'Lalb_Chr10g0104241' => 'lal', 'Lalb_Chr15g0079801' => 'lal', 'Lalb_Chr17g0340681' => 'lal', 'Lalb_Chr17g0340691' => 'lal', 'Lalb_Chr17g0346001' => 'lal', 'Lj2g0004740' => 'lja', 'Lj3g0008343' => 'lja', 'Lj4C258T9' => 'lonja', 'Lj4C822T3' => 'lonja', 'Lj5g0013458' => 'lja', 'Lj5g0023059' => 'lja', 'Lj6P730T67' => 'lonja', 'Lj7C415T12' => 'lonja', 'LjContig00141g0000877' => 'lja', 'LjContig00141g0018649' => 'lja', 'Lsat_1_v5_gn_3_120241' => 'lsa', 'Lsat_1_v5_gn_3_65760' => 'lsa', 'Lsat_1_v5_gn_8_34381' => 'lsa', 'Lsat_1_v5_gn_8_36300' => 'lsa', 'Manes.01G121000' => 'mes', 'Manes.13G153700' => 'mes', 'Manes.17G016200' => 'mes', 'Manes.17G089400' => 'mes', 'Mapoly0006s0138' => 'mpo', 'Mapoly0039s0094' => 'mpo', 'MBI03_g39996_MAGBIO' => 'mbi', 'MBI13_g04214_MAGBIO' => 'mbi', 'MBI19_g27701_MAGBIO' => 'mbi', 'MCO04G046' => 'mco', 'MD05G1001000' => 'mdo', 'MD09G1267100' => 'mdo', 'MD10G1001100' => 'mdo', 'MD10G1001200' => 'mdo', 'MD10G1001300' => 'mdo', 'MD13G1047400' => 'mdo', 'MD15G1141000' => 'mdo', 'MD16G1012700' => 'mdo', 'MD17G1254900' => 'mdo', 'MD17G1255000' => 'mdo', 'MD17G1255100' => 'mdo', 'MD17G1260200' => 'mdo', 'Medtr0482s0010' => 'mtr', 'Medtr1g076990' => 'mtr', 'Medtr4g035550' => 'mtr', 'Medtr5g040700' => 'mtr', 'Medtr5g077750' => 'mtr', 'Medtr8g022110' => 'mtr', 'Medtr8g022150' => 'mtr', 'MELO3C003278.2' => 'cme', 'MELO3C013808.2' => 'cme', 'MELO3C020044.2' => 'cme', 'Migut.E00500' => 'egut', 'Migut.E00566' => 'egut', 'Migut.H02233' => 'egut', 'Migut.H02544' => 'egut', 'MSTRG.23235' => 'ama', 'Nitab4.5_0001438g0110' => 'nta', 'Nitab4.5_0001650g0050' => 'nta', 'Nitab4.5_0001650g0070' => 'nta', 'Nitab4.5_0001822g0120' => 'nta', 'Nitab4.5_0002209g0010' => 'nta', 'Nitab4.5_0002257g0040' => 'nta', 'Nitab4.5_0003104g0040' => 'nta', 'Nitab4.5_0005124g0080' => 'nta', 'Nitab4.5_0006574g0070' => 'nta', 'Nitab4.5_0009898g0040' => 'nta', 'Nitab4.5_0020917g0020' => 'nta', 'Nn3g18430' => 'nnu', 'Nn4g24573' => 'nnu', 'Nn5g27186' => 'nnu', 'Oeu006311.1' => 'oeu', 'Oeu006316.1' => 'oeu', 'Oeu012497.1' => 'oeu', 'Oeu027939.1' => 'oeu', 'Oeu046361.1' => 'oeu', 'Oeu054206.1' => 'oeu', 'Oeu055721.1' => 'oeu', 'Os01g0877500' => 'osa', 'Os03g0716200' => 'osa', 'Os09g0449000' => 'osa', 'Os11g0234200' => 'osa', 'Peaxi162Scf00003g02037' => 'pax', 'Peaxi162Scf00025g00014' => 'pax', 'Peaxi162Scf00124g01724' => 'pax', 'Peaxi162Scf00274g00853' => 'pax', 'Peaxi162Scf00577g00006' => 'pax', 'PGR042G2215' => 'pgr', 'PGR102G2196' => 'pgr', 'PGR119G0702' => 'pgr', 'PGR142G2244' => 'pgr', 'PGR142G4168' => 'pgr', 'PGSC0003DMG400000605' => 'stu', 'PGSC0003DMG400006006' => 'stu', 'PGSC0003DMG400013247' => 'stu', 'PGSC0003DMG400013249' => 'stu', 'PGSC0003DMG400036423' => 'stu', 'PGSC0003DMG400037898' => 'stu', 'PGSC0003DMG402000629' => 'stu', 'Phvul.002G085000' => 'pvu', 'Phvul.007G114100' => 'pvu', 'Phvul.008G238400' => 'pvu', 'Phvul.011G004000' => 'pvu', 'Potri.004G134700' => 'ptr', 'Potri.008G137200' => 'ptr', 'Potri.010G101300' => 'ptr', 'Potri.013G092000' => 'ptr', 'Potri.017G135200' => 'ptr', 'Potri.018G137000' => 'ptr', 'Potri.T045600' => 'ptr', 'Pp3c15_21830' => 'ppa', 'Pp3c9_20410' => 'ppa', 'PRCOL_00006502' => 'pco', 'Prupe.1G338600' => 'ppe', 'Prupe.1G496100' => 'ppe', 'Prupe.1G496500' => 'ppe', 'Prupe.1G496700' => 'ppe', 'Prupe.3G164800' => 'ppe', 'Prupe.4G288800' => 'ppe', 'Prupe.8G002100' => 'ppe', 'Psat1g113120' => 'psa', 'Psat1g113200' => 'psa', 'Psat2g046160' => 'psa', 'Psat2g119840' => 'psa', 'Psat4g172080' => 'psa', 'Psat7g192600' => 'psa', 'PSO017G0079' => 'pso', 'PSO063G0042' => 'pso', 'PSO063G2555' => 'pso', 'PSO210G1502' => 'pso', 'PSO761G0025' => 'pso', 'PSO832G0326' => 'pso', 'QL02p059620' => 'qlo', 'QL03p039232' => 'qlo', 'QL09p001115' => 'qlo', 'QL10p037912' => 'qlo', 'RcHm_v2.0_Chr2g0092391' => 'rch', 'RcHm_v2.0_Chr2g0092501' => 'rch', 'RcHm_v2.0_Chr2g0092521' => 'rch', 'RcHm_v2.0_Chr2g0134011' => 'rch', 'RcHm_v2.0_Chr3g0450161' => 'rch', 'RcHm_v2.0_Chr3g0485271' => 'rch', 'RcHm_v2.0_Chr3g0492331' => 'rch', 'RcHm_v2.0_Chr4g0445351' => 'rch', 'RcHm_v2.0_Chr6g0249511' => 'rch', 'RcHm_v2.0_Chr6g0294291' => 'rch', 'Rhsim08G0000200' => 'rsi', 'Rhsim09G0084700' => 'rsi', 'Rhsim09G0087500' => 'rsi', 'Rhsim10G0180900' => 'rsi', 'Rhsim10G0196400' => 'rsi', 'Rhsim10G0196600' => 'rsi', 'Rhsim10G0196800' => 'rsi', 'Rhsim10G0198200' => 'rsi', 'Rhsim10G0198500' => 'rsi', 'Sabra04G0083300' => 'sbr', 'Sabra08G0104600' => 'sbr', 'Sabra10G0073900' => 'sbr', 'Sabra12G0092800' => 'sbr', 'Sabra13G0072500' => 'sbr', 'Sabra17G0111100' => 'sbr', 'Sabra17G0114100' => 'sbr', 'Sabra19G0000300' => 'sbr', 'Sabra19G0012500' => 'sbr', 'SabraMtG0000500' => 'sbr', 'SalBow2G0162' => 'sbo', 'SalBow8G1970' => 'sbo', 'Sc06g0005280' => 'sci', 'Sc11g0004670' => 'sci', 'Sc16g0009920' => 'sci', 'Sc16g0009930' => 'sci', 'Sed0006707' => 'sed', 'Sed0019363' => 'sed', 'Sed0024967' => 'sed', 'SEGI_11319' => 'sgi', 'SEGI_22597' => 'sgi', 'SEGI_30421' => 'sgi', 'SEGI_36297' => 'sgi', 'SGA_v2.0_scaffold108G30973' => 'sas', 'SGA_v2.0_scaffold12G06273' => 'sas', 'SGA_v2.0_scaffold23G10089' => 'sas', 'SGA_v2.0_scaffold23G10157' => 'sas', 'SGA_v2.0_scaffold51G18843' => 'sas', 'SHI04348' => 'shi', 'SHI16846' => 'shi', 'SHI30122' => 'shi', 'SHI38347' => 'shi', 'SMO356G0690' => 'smo', 'SMO356G0691' => 'smo', 'Solyc03g116440.3' => 'sly', 'Solyc04g007270.3' => 'sly', 'Solyc04g008420.1' => 'sly', 'Solyc11g011560.3' => 'sly', 'Sopen03g035340' => 'spe', 'Sopen04g002330' => 'spe', 'Sopen04g003570' => 'spe', 'Sopen11g006430' => 'spe', 'Sp1g28880' => 'spa', 'Sp2g13240' => 'spa', 'Sp5g21230' => 'spa', 'Sp6g22980' => 'spa', 'TAR069G0001' => 'tar', 'TAR371G0619' => 'tar', 'TAR381G0430' => 'tar', 'TAR381G0575' => 'tar', 'TAR629G3084' => 'tar', 'THA.LOC104805977' => 'tha', 'THA.LOC104811285' => 'tha', 'THA.LOC104813080' => 'tha', 'THA.LOC104824122' => 'tha', 'Thecc.01G146300' => 'tca', 'Thecc.03G278400' => 'tca', 'Thecc.08G138800' => 'tca', 'Thecc.08G166500' => 'tca', 'Thhalv10003728m.g' => 'esa', 'Thhalv10006958m.g' => 'esa', 'Thhalv10012892m.g' => 'esa', 'Thhalv10018197m.g' => 'esa', 'TPR.G11027' => 'tpr', 'TPR.G15121' => 'tpr', 'TPR.G16615' => 'tpr', 'TPR.G36435' => 'tpr', 'TPR.G39165' => 'tpr', 'TPR.G39242' => 'tpr', 'TPR.G5813' => 'tpr', 'TWI31G0341' => 'twi', 'TWI34G0742' => 'twi', 'TWI77G0649' => 'twi', 'TWI79G0263' => 'twi', 'unitig_699.g19542' => 'ugi', 'unitig_699.g19543' => 'ugi', 'unitig_699.g19576' => 'ugi', 'unitig_736.g22366' => 'ugi', 'unitig_899.g14977' => 'ugi', 'vmacro10748' => 'vma', 'vmacro18689' => 'vma', 'vmacro20635' => 'vma', 'VMungo0647G2455' => 'vmu', 'VMungo0720G2202' => 'vmu', 'VMungo1127G0395' => 'vmu', 'VMungo1215G3405' => 'vmu', 'Zm00001eb167840' => 'zma', 'Zm00001eb216130' => 'zma', 'Zm00001eb314550' => 'zma', 'Zm00001eb366330' => 'zma' ) $gf_id = 'HOM05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001174' ) $data_identifier = 'HOM05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 7, 'arhy' => (int) 12, 'ath' => (int) 6, 'atr' => (int) 14, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 11, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 4, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 23, 'fve' => (int) 6, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 7, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 7, 'psa' => (int) 6, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 10, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb366330' $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